The hotel, which will known as the Clarion from April 1, will undergo an extensive upgrade of its rooms, restaurant, conference facilities and lobby.
The move follows a decision by owner, Copenhagen Airports A/S, to enter into a new partnership with the Nordic region's leading hotel operator, Nordic Choice Hotels.
It promises that the new-look hotel will operate as a high-end brand.
"The hotel is important for many of our travellers. It's therefore vital for us that it is even more reflective of the Nordic feel and high quality that we want to offer those travellers," explains Thomas Woldbye, CEO of Copenhagen Airports A/S.
"Nordic Choice Hotels can deliver that, and I'm certain we've found the right partner."
Woldbye thanked Hilton for its collaboration since the hotel opened in 2001, adding: "We've enjoyed a excellent collaboration with Hilton, which has operated the hotel professionally and with a high standard, and we're delighted that the skilled employees will be able to continue under the new Clarion brand."
Nordic Choice Hotels is Scandinavia's largest operator of airport hotels, and on taking over the operation of the hotel it will undertake a major upgrade.
"Clarion Hotel is our high-end chain with a strong full-service concept, and it sets a high standard for design, interiors, art, food and drink," says Petter Stordalen, owner of Nordic Choice Hotels.
"It's our ambition that this hotel should be reborn as an even bigger success.
"Clarion Hotel Arlanda Airport has been crowned Sweden's best business hotel and Europe's most luxurious airport hotel, and experiences from there will benefit the hotel at Copenhagen Airport."